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  EMBOSS: myseq
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myseq
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<H2>
    Function
</H2>
<!--#include file="inc/myseq.ione" -->

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DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
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<H2>
    Description
</H2>

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        This is what the user looks at to find out if this program will do what he wants. 
        Long description.
        Why it is useful.
        When it should/shouldn't be used.
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Simple sequence reading application as a template for writing new programs.


<H2>
    Algorithm
</H2>

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        Algorithms
	  Pseudocode/Vague description/Handwaving/web links to useful pages
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None.



<H2>
    Usage
</H2>

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	Example usage, as run from the command-line.
        Many examples illustrating different behaviours is good.
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<!--#include file="inc/myseq.usage" -->



<H2>
    Command line arguments
</H2>

<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
<!--#include file="inc/myseq.ihelp" -->
</pre>
</td></tr></table>
<P>
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DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
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<H2>
    Input file format
</H2>

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        This includes example input file formats.
        This should be a detailed description and example - assume
        someone will want to parse this file and will want to know what
        happens in unusual cases - null input, etc. 
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<b>myseq</b> reads any normal sequence USAs.

<p>

<!--#include file="inc/myseq.input" -->





<H2>
    Output file format
</H2>

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        This includes example output file formats.
        This should be a detailed description and example - assume
        someone will want to parse this file and will want to know what
        happens in unusual cases - null output, errors etc. 

        If you wish to include the standard description of the avalable
	report formats, use:
include file="inc/reportformats.ihtml"
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<b>myseq</b> 
outputs a graph to the specified graphics device. 
outputs a report format file. The default format is ...


<p>

<!--#include file="inc/myseq.output" -->





<H2>
    Data files
</H2>

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        Any data files used (e.g. translation table file)
        This includes example data file formats if they are
        not obvious.

	If you wish to include the standard description of what data
	files are and how to use embossdata to inspect and retrieve
	them, use:
include file="inc/localfiles.ihtml"
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None.

<H2>
    Notes
</H2>

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        Restrictions.
        Interesting behaviour.
        Useful things you can do with this program.
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None.







<H2>
    References
</H2>

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        Bibliography for methods used.
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None.








<H2>
    Warnings
</H2>

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        Potentially stupid things the program will let you do.
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None.







<H2>
    Diagnostic Error Messages
</H2>

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        Error messages specific to this program, eg:
        "FATAL xxx" - means you have not set up the xxx data using program <b>prog</b>.<p>
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None.







<H2>
    Exit status
</H2>

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        Description of the exit status for various error conditions
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It always exits with status 0.








<H2>
    Known bugs
</H2>


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        Bugs noted but not yet fixed.
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None.








<!--
<H2>
    See also
</H2>
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<!--#include file="inc/myseq.isee" -->
<!-- 
        Add any comments about other associated programs (to prepare
        data files?) that seealso doesn't find. 
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<H2>
    Author(s)
</H2>

<!--#include virtual="/apps/inc/price.address" -->

<H2>
    History
</H2>

<!--#include file="inc/myseq.history" -->



<H2>
    Target users
</H2>

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        For general users, requested by one user, for EMBOSS site
        maintainers, for EMBOSS developers etc.
        eg:
        "This program is intended to be used by everyone and everything,
        from naive users to embedded scripts." 
	Which is easy to include using:
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<!--#include virtual="/apps/inc/target.itxt" -->











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